Progress 12/15/13 to 12/14/15
Outputs
Target Audience:During this reporting period we made efforts to disseminate our research findings widely. The project director gave research seminars describing parts of this work at the University of California Davis, Cornell University, and Hamilton College. In addition to these seminars, the work was presented as a guest lecture in an introductory One Health class at the UC Davis vet school, as a poster at the USDA NIFA project directors meeting and as an oral presentation at the American Ornithologists Union annual conference. As a result of these presentations, the results obtained have been shared with academics, conservation groups, funding agencies, legislators, and students. Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided?The project provided many opportunities for training and professional development. For the project director, these opportunities included learning new skills, such as stable isotope sampling, analysis of animal location data, and DNA sequencing, along with development opportunities, such as guest lecturing, presenting seminars on the work, and attending two conferences to present the work. A number of other graduate students, undergraduate students, technicians, and postdocs have also been involved with parts of the work and have benefited from the project by learning new techniques that they may use in their own projects. How have the results been disseminated to communities of interest?The project director presented the work in seminars at the University of California Davis, Cornell University, and Hamilton College and in a guest lecture to an introductor One Health class at the UC Davis Vet School. The project director also presented parts of this project as a poster at the USDA NIFA project director's meeting and as an oral presentation at the American Ornithologists Union meeting. Papers from the project are in the process of being produced and will serve to further disseminate the results to a wide audience. At present, one paper on host ecology and campylobacer associations is submitted and a second on the full genome sequences of isolates is near submission. At least two more papers are in preparation (all data is collected) and should be submitted over the coming months. What do you plan to do during the next reporting period to accomplish the goals?
Nothing Reported
Impacts
What was accomplished under these goals?
We made significant progresss on each of our three goals over the two year project period: 1. We successfully sequenced the full genome of >100 isolates of Campylobacter jejuni from crows and livestock in our study site and have now compared those sequences to known human pathogens to demonstrate that there is strong evidence for some cross species transmission from crows. The results of that effort are now written up in draft form and should be submitted for publication early in 2016. 2. We successfully tracked migratory crows with satellite transmitters and now have reliable data (with thousands of locations) on the migratory origin and movement paths employed by some crows at our site. Using those tracked individuals as a calibration set, we also identified the migratory origin of >500 passively molted feathers from under the large winter roost at our field site. We know have a very good estimate of the percentage of the roost comprised of birds from different locations and the amount of population mixing that occurs in the winter along with the genome sequences of isolated Campylobacter jejuni from migrants and residents. Those data are complete at this point and will be analyzed and written up for publication over the next six months. 3. We successfully combined information on year round Campylobacter infection prevalence, winter movement data, and social behavior to identify the links and influence between host ecology and cross species transmission risk at our field site. The results of that effort are currently under review for publication and should be available for general consumption in 2016.
Publications
- Type:
Journal Articles
Status:
Under Review
Year Published:
2016
Citation:
Influence of host ecology and behavior on Campylobacter jejuni prevalence and environmental contamination risk in an urbanophilic wild bird. Submitted to Applied & Environmental Microbiology.
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Progress 12/15/13 to 12/14/14
Outputs
Target Audience: In this reporting period, we were focused on launching the project and beginning data collection. We did not communicate extensively with target audiences because we did not have major results to report. We did, however, discuss the project goals and aims informally with conservation and disease biologists at the joint meeting of the American Ornithologists Union and Cooper Ornithological Society in Estes Park, Colorado and at the annual Animal Behavior Society meeting in Princeton, NJ. Each of these venues provided an opportunity to get feedback on our techniques that has strengthened the project going forward and provided an opportunity to build connections with individuals who will be able to help in distributing results from our project as they come in. We expect to expand our interactions with target audiences as project results accumulate in year two. Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided? In this reporting period, there were substantial opportunities for training and professional development for the project director, for students, and for technicians who worked on various aspects of data collection and analysis. We list these opportunities with short descriptions below: Training opportunities in year one: Training for both the project director and a lab technician in preparation and submission of samples for isotopic analysis provided by the UC Davis Stable Isotope Facility. Using this training, we are currently processing and submitting >300 feather samples for isotopic analysis to understand migratory distance and population mixing in accord with project goals 2 & 3. Training for both the project director, one lab technician, and one graduate student in a variety of molecular biology tools and techniques associated with sampling and testing for bacterial infection, DNA extraction and PCR, and sequencing techniques and analysis. This training has been accomplished both through work in the sponsor (Townsend’s) lab and through interactions with collaborating labs in the UC Davis Vet School. Training for the project director in epidemiological modeling through interactions with modelers in the UC Davis Vet School. In year one, this training was largely focused on becoming familiar with the techniques and approaches used to model infection dynamics. In year two, this work will grow into incorporating the original data collected as part of this project into modeling work in collaboration with one faculty member and one graduate student in the UC Davis Vet School. Training for the project director, a lab technician, and two graduate students in a variety of field techniques including capture, handling, and biological sampling of wild birds, tracking and monitoring of wild birds, and application of telemetry, GPS, and satellite transmitters to wild birds. Professional development opportunities in year one: In this reporting period, the project director attended two conferences that provided opportunities for informal feedback and professional networking associated with the project goals. During year one, the project director was the organizer and often the presenter at an ongoing lab discussion group in the wildlife department on campus that brought together a undergraduates, graduate students, postdocs, and faculty with similar research interests. That group often discussed plans and results associated with our project, among other topics, and provided a professional development opportunity for a large group of current and future scientists. How have the results been disseminated to communities of interest? In year one, we did not make major efforts to disseminate our work to communities of interest because we did not have any well developed results to report. As described in this report, we begun to amass enough data to draw some conclusions and we expect to have more data in place over the next six months. Thus, we will devote much more time to disseminating results to interested communities during year two. We expect to accomplish this goal by presenting results of this project at both national conferences and to local groups and by publishing our results in appropriate journals during year two. What do you plan to do during the next reporting period to accomplish the goals? Much of year one was spent fine-tuning data collection and lab procedures. For the most part, data collection in year two will build directly on this foundation and we expect our sample sizes for each data set to increase now that the project is running smoothly. In addition to collecting more data of each type described above, we have three main goals for year two: Work with modelers in the UC Davis vet school to build a biologically realistic model of C. jejuni transmission. This work was initiated in year one, but we have only recently accumulated enough data to really tackle this project in a meaningful way. More time will be devoted to this objective in year two. Organize, analyze, and write up results from each objective for publication. The majority of data collection for each objective will be completed in the first 6-8 months of year two. The remainder of year two will be used to analyze results and write and submit papers for publication. Communicate results to target audiences. We expect to spend much more effort communicating our results to target audiences in year two. In part, this will be accomplished by publication in appropriate journals. We also plan to attend at least two conferences in year two and to formally present results from this project.
Impacts
What was accomplished under these goals?
In industrialized countries, most gastroenteritis is caused from infection by Campylobacter jejuni. In the United States alone, up to 2.4 million people may be infected each year and infections can result in 5-7 days of vomiting, diarrhea, and abdominal pain. Typically, humans get infections from eating poultry that is contaminated and improperly cooked. Recently, intense effort has been devoted to understanding the initial route of flock infection by studying the dynamics of C. jejuni transmission between wild animals, domestic animals, and humans. Wild birds are known to harbor C. jejuni and may serve as a major reservoir of C. jejuni. When these birds interact with domestic animals (perhaps drawn by easy access to food), they may serve as the initial vector of domestic animal infection. Understanding these interactions could lead to cost effective management plans. In our project, we are studying the dynamics of C. jejuni infection and the potential for cross-species infection, produce contamination, and long distance movement of bacterial isolates in wild American crows in Davis, California. Our project has three major objectives. 1. Determine if strains of C. jejuni found in wild crows are the same as those found in samples from poultry, livestock, and humans. A) We are going beyond the simple testing for C. jejuni often employed in studies of wildlife by sequencing the entire genome of isolates from crows and from local domestic animals and then comparing those genomes to sequences derived from human infections. B) We have now collected a total of 232 crow fecal samples from adults, juveniles, migrant, and local birds. We have also submitted samples from ~20 isolates collected from local poultry. We are still collecting new isolates and many samples are queued for sequencing. C) Of the 232 samples tested, 133 (57%) tested positive for C. jejuni and these samples have been submitted for full genome sequencing. Genomes for the first 81 of these isolates are complete. Preliminary results suggest that some crow C. jejuni strains are indeed potential human pathogens. For example, we found strains that included five major genetic variants associated with C. jejuni virulence in humans. D) At this point, our results are consistent with the idea that wild birds may harbor human pathogenic C. jejuni, but they also suggest that it will be important to characterize particular strains of bacteria, rather than just testing for presence or absence of C. jejuni. 2. Assess the potential for long distance transmission of non-local C. jejuni strains by crows. A) Some crows in our winter roost population are migrants and, as such, may distribute C. jejuni over long distances during their migration. To understand this risk, we have been collecting data that will allow us to quantify both the movement and migration behavior of crows and the similarity of bacterial isolates carried by migrants and residents. B) In year one, we captured adult crows during the winter and affixed solar satellite location transmitters. Second, we collected feathers from 315 crows for use in stable isotope analysis to determine migratory origin. We initially submitted 10 feather samples in a pilot test. We are currently finishing preparation of the remaining 305 samples (75 known residents, 30 known non-local birds from various locations, and 200 from birds of unknown location). We also built a data-set that will allow us to compare the similarity of isolates collected from local and non-local birds. So far, we have received full genome sequences mainly from local birds. Isolates from known migrants are queued for sequencing now. C) In year one, we deployed three satellite transmitters. Of these three birds, one was a long distance migrant. That bird left our roost in March, spent time at another California roost, and then migrated to a breeding location in southern Oregon (Figure 1). The stable isotope results from our pilot sample of ten feathers were also promising. Of five unknown location feathers submitted, four had local isotopic signatures, but one had a value that suggested a growth location in northern Washington State or southern Canada. Figure 1. Three crows were captured and fitted with transmitters in Davis, CA in 2013 (A). One crow later moved to a second crow roost ~50 miles away (B) and then migrated to a breeding site in southern Oregon ~300 miles away (C). Heat maps illustrate habitat use patterns based on >1,000 independent locations collected from these three birds in 2014. D) Some of the birds in our winter roost are, in fact, long distance migrants. Satellite data demonstrated one migrant from Oregon and isotopic data suggested one migrant from Washington or southern Canada. We expect both of these data-sets to grow substantially in the first few months of year two as we deploy up to 20 additional transmitters and receive the results for 305 feathers collected in year one. 2. Develop a biologically informed and spatially explicit epidemiological model of cross-species infection dynamics to generate predictions and management recommendations aimed ad reducing the incidence of C. jejuni infection. A) If wild birds, such as crows, act as important vectors of C. jejuni infection it may be possible to reduce domestic animal infection—and eventual human infection—by managing interactions between wildlife and domestic animals. To that end, we are working to development a compartmental SIRS-type stochastic model parameterized by biologically relevant data about movement, habitat use, disease prevalence, and host density. In year one, we have made good progress toward collecting the data that will be used to parameterize our model. B) Much of the data describe in objectives one and two above will be used in model construction. In addition to those data, we have collected a variety of other data that describe seasonal dynamics of crow behavior and C. jejuni infection. Crow habitat use. We received >1,000 locations from satellite transmitters, from which we have constructed heat maps describing habitat use (Figure 1). Overall C. jejuni prevalence, infection rates by class, and seasonal variation in infection. We have now tested 232 crow fecal samples for C. jejuni infection across the entire annual cycle and from both adults and nestlings; these collection efforts are continuing in year two. Crow density and clustering behavior. The large winter roosts that crows form are potentially very important in bacterial transmission because a large number of individuals are in extremely close proximity for an extended time, potentially increasing intra-specific transmission and resulting in higher overall C. jejuni prevalence. C) Status of data that will be incorporated into our model. Crow habitat use. Satellite tracked crows foraged widely over the urban areas of the city, forayed on agricultural fields, at a poultry facility and sheep barn, and spent a large proportion of their time near a dairy feedlot. Overall C. jejuni prevalence, infection rates by class, and seasonal variation in infection. Infection varied seasonally, with lower prevalence during the fall than at any other time of the year (X2 = 4.32, P = 0.03). Finally, we found that infection rate is higher for nestlings than for adults (Fisher’s exact test, P = 0.03). Crow density and clustering behavior. Weekly roost counts reveal that the roost begins to form in early October, reaches maximum size of 8-10,000 birds by January 1st, begins to decline by late February, and is undetectable by early May. D) Taken together, our results suggest that mitigating contact between crows and domestic animals during the winter months, when infection rates are high but crows have not yet dispersed to breeding grounds may be an effective intervention. In year two, these data will be incorporated into our modeling framework, allowing us to draw stronger conclusions.
Publications
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